BIOPHOTONICS

Electromagnetic wave propagation: plane waves, spherical waves, phase velocity, irradiance, wave packets, group velocity, coherence length, interference.
Scalar diffraction theories: the Kirchhoff formulation, the Rayleigh-Somrnerfeld formulation, the Huygens-Fresnel principle.
Geometrical optics: Optical path length, the principle of Fermat, ideal imaging systems, matrix methods in paraxial imaging, cardinal points and planes.
Apertures and stops, image-forming instruments, brightness and illumination of images, intensity fluctuations, detection noise.
The Debye integral representation of focused fields, irradiance distribution near focus (three-dimensional point spread function). Resolving power: the Rayleigh criterion. Minimum angular separation, visual acuity, phototransduction.
Transmitted light microscopy: angular spectrum of plane waves, diffraction gratings, abbe theory and resolution. Phase contrast, dark field, and differential interference contrast microscopy.
Fluorescence microscopy: molecular spectra, Jablonski diagram, Stokes' shift, life time and quantum efficiency, saturation of the excited state. Structure of the conventional fluorescence microscope.
Confocal microscopy: lateral resolution and axial resolution in the classical limit; optical sectioning and volume reconstruction; physical principles and applications of 2-photon excitation; advantages and disadvantages of different confocal systems.
Stimulated emission depletion (STED) nanoscopy and super-resolution.
Selected biophotonics applications: optical recording of changes in ion concentration. Optical sensors of Ca2+ ions, protons and other physiologically relevant ionic species. Imaging of Ca2+ at one and two wavelengths; local control of the concentration of Ca2+ and other active molecular species by UV photolysis of caged compounds; FRET, FRAP.
Intravital microscopy: biosensors, optochemogenetics, photodynamic therapy of cancer.